5CR6 | pdb_00005cr6

Structure of pneumolysin at 1.98 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.266 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 
    0.249 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

The Crystal Structure of Pneumolysin at 2.0 angstrom Resolution Reveals the Molecular Packing of the Pre-pore Complex.

Marshall, J.E.Faraj, B.H.Gingras, A.R.Lonnen, R.Sheikh, M.A.El-Mezgueldi, M.Moody, P.C.Andrew, P.W.Wallis, R.

(2015) Sci Rep 5: 13293-13293

  • DOI: https://doi.org/10.1038/srep13293
  • Primary Citation Related Structures: 
    5CR6, 5CR8

  • PubMed Abstract: 

    Pneumolysin is a cholesterol-dependent cytolysin (CDC) and virulence factor of Streptococcus pneumoniae. It kills cells by forming pores assembled from oligomeric rings in cholesterol-containing membranes. Cryo-EM has revealed the structures of the membrane-surface bound pre-pore and inserted-pore oligomers, however the molecular contacts that mediate these oligomers are unknown because high-resolution information is not available. Here we have determined the crystal structure of full-length pneumolysin at 1.98 Å resolution. In the structure, crystal contacts demonstrate the likely interactions that enable polymerisation on the cell membrane and the molecular packing of the pre-pore complex. The hemolytic activity is abrogated in mutants that disrupt these intermolecular contacts, highlighting their importance during pore formation. An additional crystal structure of the membrane-binding domain alone suggests that changes in the conformation of a tryptophan rich-loop at the base of the toxin promote monomer-monomer interactions upon membrane binding by creating new contacts. Notably, residues at the interface are conserved in other members of the CDC family, suggesting a common mechanism for pore and pre-pore assembly.


  • Organizational Affiliation
    • Department of Infection, Immunity and Inflammation, University of Leicester, PO Box 138, Leicester, LE1 9HN UK.

Macromolecule Content 

  • Total Structure Weight: 52.93 kDa 
  • Atom Count: 3,907 
  • Modeled Residue Count: 467 
  • Deposited Residue Count: 471 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PneumolysinA [auth D]471Streptococcus pneumoniaeMutation(s): 2 
Gene Names: plySPD_1726
Membrane Entity: Yes 
UniProt
Find proteins for Q04IN8 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466))
Explore Q04IN8 
Go to UniProtKB:  Q04IN8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04IN8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.266 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 0.249 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.006α = 90
b = 127.71β = 90
c = 172.285γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom097828/z/11/z
Medical Research Council (United Kingdom)United KingdomPhD project grant

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description